Aliging sequences using BLAST is the most common task performed in bioinformatics. Here is how you can do it using BioPerl:

#!/usr/bin/perl
use strict;
use warnings;
use Bio::Perl;

# get sequence given an identifier or accession number
my $so = get_sequence('swiss',$ARGV[0]);

# get blast the sequence
my $blast_result = blast_sequence($so);

# write blast results into a file
write_blast(">$ARGV[1]",$blast_result);

usage:

$ chmod 755 blastseq.pl
$ perl blastseq.pl PYGM_HUMAN pygm.blast

The above example retrieves a sequence from Swiss-Prot and then blasts the retrieved sequence against NCBI blast server. The following example blasts a given sequence against NCBI blast server.

#!/usr/bin/perl
use strict;
use warnings;
use Bio::Perl;

# get sequence
my $blast_result = blast_sequence('MFVEGGTFASEDDDSASAEDE');

# write output to file
write_blast(">$ARGV[0]",$blast_result);

usage:

$ chmod 755 blastseq2.pl
$ perl blastseq2.pl test.blast

The next example takes a fasta file as input which is used to blast against NCBI blast server.

#!/usr/bin/perl
use strict;
use warnings;
use Bio::Perl;
use Bio::SeqIO;

# create sequence object from the fasta file
my $s = Bio::SeqIO->new(
        -file => $ARGV[0],
        -format => "fasta"
);

while (my $st = $s->next_seq)
{
        # uncomment to print fasta sequence
        # print $st->seq;

        # blast against NCBI blast server
        my $blast_result = blast_sequence($st->seq);

        # write blast results to the specified file
        write_blast(">$ARGV[1]",$blast_result);
}

usage:

$ chmod 755 blastseq3.pl
$ perl blastseq3.pl pygm.fasta pygm.blast